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GUNC: detection of chimerism and contamination in prokaryotic genomes.

Askarbek Orakov; Anthony Fullam; Luis Pedro Coelho; Supriya Khedkar; Damian Szklarczyk; Daniel R Mende; Thomas SB Schmidt; Peer Bork

v1.0.2 Features

  • GUNC can now be run with GTDB database
  • Added option to download GTDB_GUNC database
  • Input file options can be gene_calls (faa) instead of fna if --gene_calls flag is set
  • Input genecalls can be gzipped
  • Output maxCSS file is now sorted


  • Fix version of dependancy: requests>=2.22.0 (older versions not compatable)
  • Better error message if gunc_db does not exist
  • checkm_merge didnt work with unless checkm qa was run with -o 2


  • Documentation updates
    • Links to synthetic datasets added
    • Citations for diamond and prodigal added
    • Clarified how checkM should be run for checkm_merge
    • Corrected command for download_db
  • Check if fasta is given with -f option instead of list of filepaths

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